Crystal structure of E.coli GDP-fucose synthetase (and complexes thereof) and methods of identifying agonists and antagonists using same

ABSTRACT

The present invention provides for crystalline GFS. The crystal structure of GFS has also been solved using such material. Models based upon such crystal structure are also provided. Methods of identifying inhibitors of GFS activity using such models are also disclosed.

This application claims priority from U.S. application Ser. No.60/096,452, filed Aug. 13, 1998.

BACKGROUND OF THE INVENTION

Fucose is found widely distributed in the complex carbohydrates andglycoconjugates of bacteria, plants, and animals. In these organisms itplays diverse roles, ranging from its involvement in nodulation inAzorhizobium [1] to development of shoots in Arabidopsis [2] to adhesionof leukocytes to activated endothelia in humans as part of the selectinligand [3]. In humans a defect in GDP-fucose biosynthesis is responsiblefor the immune disorder Leukocyte Adhesion Deficiency type II [4, 5, 6].Fucose is added to these glycoconjugates by specific transferases thatuse GDP-fucose as the sugar donor. GDP-fucose in turn is synthesizedprimarily from GDP-mannose in a three-step reaction involving twoenzymes as shown in FIG. 1. The first step is the oxidation at C4 of themannose ring and subsequent reduction at C6. This is carried out by aNADP⁺ dependent enzyme, GDP-mannose 4,6 dehydratase (GMD) [7, 8, 9]. Thenext two steps of the reaction, the epimerization at C3 and C5 of themannose ring and the subsequent NADPH dependent reduction at C4 to yieldGDP-fucose, are carried out by a single dual function enzyme, GDP-fucosesynthetase (GFS) [9, 10, 11]. In E. coli this enzyme is encoded by thefcl gene, previously known as wcaG [12, 13]. It is in these final twosteps that GDP-fucose biosynthesis differs from synthesis of other deoxysugars derived from dTDP-glucose and CDP-glucose. In the latterpathways, separate epimerase and reductase enzymes encoded byindependent genes perform the roles of the dual functionepimerase-reductase of the GDP-fucose pathway (reviewed in [14]).

The human homologue of GFS has recently been identified as the FXprotein [1]. As with the E. coli enzyme it is a homodimer that bindsNADP(H) and catalyzes both the epimerization and reduction ofGDP-4-keto, 6-deoxy-mannose. Human GFS has 29% identity to the E. coliprotein. More distantly related to both the human and E. coli enzymes isUDP-galactose-4-epimerase GalE), which catalyzes the reversibleepimerization of UDP-glucose to UDP-galactose. Essential to catalysis isa tightly bound NAD⁺ that is reduced and then oxidized during thecatalytic cycle. UDP-galactose 4-epimerase is a member of the shortchain family of dehydrogenase/reductases (SDR) (reviewed in [15]). Thisfamily of enzymes catalyzes a diverse set of enzymatic reactionsspanning 5 E.C. classes using a conserved set of active site residuesincluding a Ser-Tyr-Lys catalytic triad.

It would, therefore, be desirable to determine the structure of E. coliGDP-fucose synthetase in order to facilitate the identification anddevelopment of agonists and antagonists of GFS enzyme activity in humansand other species.

SUMMARY OF THE INVENTION

We have determined the structure of GDP-fucose synthetase from E. coliat 2.2 Å resolution. The structure of GDP-fucose synthetase is closelyrelated to that of UDP-galactose 4-epimerase and more distantly to othermembers of the short chain dehydrogenase/reductase family. We have alsodetermined the structures of the binary complexes of GDP-fucosesynthetase with its substrate NADPH and its product NADP⁺. Thenicotinamide cofactors bind in the syn or anti conformations,respectively.

GDP-fucose synthetase binds its substrate, NADPH, in the properorientation (syn) to transfer the pro-S hydride. We have observed asingle binding site in GDP-fucose synthetase for the second substrate,GDP-4-keto, 6-deoxy-mannose. This implies that both the epimerizationand reduction reactions occur at the same site on the enzyme. As for allmembers of the short-chain family of dehydrogenase/reductases,GDP-fucose synthetase retains the Ser-Tyr-Lys catalytic triad. Wepropose that this catalytic triad functions in a mechanisticallyequivalent manner in both the epimerization and reduction reactions.Additionally, the x-ray structure has allowed us to identify otherresidues potentially substrate binding and catalysis.

The present invention provides for crystalline GFS. Preferably, the GFSis E. coli GFS, although GFS from other species are also included withinthe invention. In certain embodiments, the GFS is recombinant GFS and/orcomprises the mature sequence of naturally-occurring GFS.

Other embodiments provide for a crystalline composition comprising GFSis association with a second chemical species. Preferably, the secondchemical species is selected from the group consisting of NADPH, NADP+and a potential inhibitor of GFS activity.

Yet other embodiments provide for a model of the structure of GFScomprising a data set embodying the structure of GFS. Preferably, suchdata set was determined by crystallographic analysis of GFS, includingpossibly by NMR analysis. In certain embodiments, the data set embodiesa portion of the structure of GFS, including without limitation theactive site of GFS.

Any available method may be used to construct such model from thecrystallographic and/or NMR data disclosed herein or obtained fromindependent analysis of crystalline GFS. Such a model can be constructedfrom available analytical data points using known software packages suchas HKL, MOSFILM, XDS, CCP4, SHARP, PHASES, HEAVY, XPLOR, TNT,NMRCOMPASS, NMRPIPE, DIANA, NMRDRAW, FELIX, VNMR, MADIGRAS, QUANTA,BUSTER, SOLVE, O, FRODO, RASMOL, and CHAIN. The model constructed fromthese data can then be visualized using available systems, including,for example, Silicon Graphics, Evans and Sutherland, SUN, HewlettPackard, Apple Macintosh, DEC, IBM, and Compaq. The present inventionalso provides for a computer system which comprises the model of theinvention and hardware used for construction, processing and/orvisualization of the model of the invention.

Further embodiments provide a computer system comprising computerhardware and the model of the present invention.

Methods are also provided for identifying a species which is an agonistor antagonist of GFS activity or binding comprising: (a) providing themodel of the present invention, (b) studying the interaction ofcandidate species with such model, and (c) selecting a species which ispredicted to act as said agonist or antagonist. Species identified inaccordance with such methods are also provided.

Other embodiments provide: (1) a process of identifying a substance thatinhibits GFS activity or binding comprising determining the interactionbetween a candidate substance and a model of the structure of GFS, or(2) a process of identifying a substance that mimics GFS activity orbinding comprising determining the interaction between a candidatesubstance and a model of the structure of GFS. Substances identified inaccordance with such processes are also provided.

The study of the interaction of the candidate species with the model canbe performed using available software platforms, including QUANTA,RASMOL, O, CHAIN, FRODO, INSIGHT, DOCK, MCSS/HOOK, CHARMM, LEAPFROG,CAVEAT (UC Berkley), CAVEAT (MSI), MODELLER, CATALYST, and ISIS.

Other embodiments provide a method of identifying inhibitors of GFSactivity by rational drug design comprising: (a) designing a potentialinhibitor that will form non-covalent bonds with one or more amino acidsin the GFS sequence based upon the crystal structure co-ordinates ofGFS; (b) synthesizing the inhibitor; and (c) determining whether thepotential inhibitor inhibits the activity of GFS. In other preferredembodiments, the inhibitor is designed to interact with one or moreamino acids selected from the group consisting of Arg12, Met14, Val15,Arg36, Asn40, Leu41, Ala63, Ile86, Gly106, Ser107, Ser108, Cys109,Tyr136, Lys140, Asn165, Leu166, His179, Val180, Leu184, Val201, Trp202,Arg209, and Lys283.

Agonists and antagonists identified by such methods are also provided.

A process is also provided of identifying a substance that inhibitshuman FX protein activity or binding comprising determining theinteraction between a candidate substance and a model of the structureof GFS of the present invention.

Other embodiments provide for a method of identifying inhibitors ofhuman FX protein activity by rational drug design comprising:

(a) designing a potential inhibitor that will form non-covalent bondswith one or more amino acids in the GFS sequence based upon the crystalstructure co-ordinates of crystalline GFS of the present invention;

(b) synthesizing the inhibitor; and

(c) determining whether the potential inhibitor inhibits the activity ofhuman FX protein.

In preferred embodiments, the inhibitor is designed to interact with oneor more amino acids in the GFS sequence selected from the groupconsisting of Arg12, Met14, Val15, Arg36, Asn40, Leu41, Ala63, Ile86,Gly106, Ser107, Ser108, Cys109, Tyr136, Lys140, Asn165, Leu166, His179,Val180, Leu184, Val201, Trp202, Arg209, and Lys283.

Agonists and antagonists identified by such methods are also provided.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1: The GDP-fucose biosynthetic pathway. The enzymes catalyzing thesteps are shown above the arrows. GMD-GDP-mannose 4,6 dehydratase, is anNADP⁺ dependent enzyme in which the NADP⁺ is reduced and oxidized duringthe catalytic cycle. GFS-GDP-fucose synthetase (GDP-4-keto-6deoxy-mannose 3,5 epimerase 4-reductase).

FIG. 2: A) Stereo ribbon representation of GFS monomer showing boundNADP⁺ as a ball-and-stick. The N-terminus of the protein is labeled,N-ter. The secondary structural elements are labeled, strands withnumbers and helices with letters, proceeding from the N-terminus towardthe C-terminus. NADP+ is shown in a ball and stick representation. B)Ribbon representation of the GFS dimer showing the extensive interface.The figure dimer is viewed looking down the two fold. One monomer is inred, the other in blue. Interacting strands and helices are labeled asin 2A. The figures were made using MOLSCRIPT [49] and rendered usingRASTER3D [50].

FIG. 3: Stereo C-α trace of GFS, shown in blue, superimposed on GalE,shown in red. In each case the bound co-factor is shown as aball-and-stick with the same color scheme as the protein. On GFS, everytenth Coc is shown as a ball and numbered where possible.

FIG. 4: Quanta was used to superimpose E. coli UDP-galactose 4 epimerase(GaIE) and E. coli GDP-fucose synthetase (coli_GFS) as shown in FIG. 3.The two sequences were then aligned based upon the structural alignmentand the human GDP-fucose synthetase (human_GFS) amino acid sequence wasaligned to this pair. Identical residues are boxed in red, homologous ingrey, and residues shared between two of the three proteins are boxed inblue.

FIG. 5: A) Stereo ball-and-stick representation of the bonding of NADP⁺to GFS. The protein is shown in dark green and the co-factor in blue.Water molecules are shown as red balls and potential hydrogen bondsshown as thin black lines. B) A close up view of the NADP(H) binding.The bound NADPH is shown with thick bonds and the bound NADP⁺ in thinbonds.

FIG. 6: A ball and stick representation of GDP-4keto 6deoxy mannosebinding model. The proposed binding site residues are shown with darkbonds and the substrate/NADPH nicotinamide ring shown with light graybonds.

FIG. 7: The potential mechanism of the reduction (upper) andepimerization (lower) reactions catalyzed by GDP-fucose synthetase.Tyr136 plays the central role in donating a proton during reduction andstabilizing the negatively charged enediol during epimerization. Thisfacilitates both reactions at a single active site. Ser107 assists alongwith interactions from Lys140 and the nicotinamide ribose (not shown).Alternatively Ser107 may function as part of a proton shuttle withTyr136 as proposed for GalE [34].

FIG. 8: A) Typical M AS electron density after modification withSOLOMON, contoured at 1.5σ. Part of the final refined GFS model is shownin density for reference. B) 2F_(O)−F_(C) electron density for NADPphased with the rigid body refined uncomplexed GFS model. The finalrefined model for NADP⁺ is shown for reference. C) 2F_(O)−F_(C) densityfor NADPH phased with the rigid body refined, uncomplexed, GFS model.The final refined NADPH coordinates are shown for reference.

DETAILED DESCRIPTION OF THE INVENTION AND PREFERRED EMBODIMENTS

Results and Discussion

GDP-Fucose Synthetase is a Member of the Short Chain Family ofDehydrogenases-Reductases.

The GFS monomer forms a roughly two domain structure that provides theenzyme with the ability to bind co-factor and substrate (FIG. 2 a). TheNADP(H) binding domain is the larger of the two and contains a centralsix stranded β-sheet flanked by two sets of parallel α-helices, commonto the family of NAD(P) binding proteins (reviewed in [16]). The second,predominantly C-terminal domain is smaller and is responsible forbinding substrate. It extends away from the other domain and forms aglobular cluster of three alpha-helices and two small beta-sheets.

The N-terminal domain begins with an alternating alpha/beta repeatforming the first five strands and four flanking helices labeled in FIG.2 a as 1-A-2-B-3-C-D4-E-5. Residue Asn165 marks the first transitioninto the second, substrate binding domain, where it enters a shortbeta-strand (strand 6), a 12 residue loop, helix F, and two more strands(strands 7 and 8). At that point the chain returns to the first domainforming helices G and H and the final strand of the central β-sheet,strand 9. The remaining residues of GFS form the bulk of the substratebinding domain and consist of the secondary structural elements10-I-11-12-J-K terminating with a short piece of coil.

The structure of GFS reveals it to be a member of the short chaindehydrogenase/reductase (SDR) family of enzymes (reviewed in [15]). Thisfamily of enzymes catalyze diverse sets of reactions using a conservedcore tertiary protein fold and a serine, tyrosine, lysine triad ofcatalytic residues. GalE belongs to the SDR family and forms its ownbranch with enzymes that catalyze dehydrogenations, dehydrations, andepimerizations and isomerization. The relationship between E. coli GFS,previously known as YEFB, and GalE has been previously noted [17] andGFS has been assigned to the GalE branch of SDRs based upon sequencehomology. Consistent with this observation the structures of GFS andGalE are closely related. The overall sequence identity between GalE andGFS is 25%, resulting in structures with a RMS difference in 184 Cαpositions of only 0.8 Å (FIG. 3). Whilst most of the secondarystructural elements of the two enzymes superimpose well there are alsosome significant differences.

The first large difference occurs after the N-terminalstrand-helix-strand in which GalE has a 22 residue insertion, forming anadditional flanking helix and strand at the front of the molecule (seeFIG. 4 for amino acid alignment). This insertion provides residues inGalE which interact with the adenine ribose of NAD(H) [18] and wouldcause steric clashes if NADP⁺ were to bind to GalE. In the absence ofthis loop, Arg36 of GFS directly hydrogen bonds with the C2′ phosphateof NADP(H) and provides GFS with the ability to distinguish NAD(H) fromNADP(H). The absence of this loop in GFS results in NADPH binding in amore solvent exposed arrangement, consistent with the observation thatNADPH binds, then transfers the hydride, and is then released as NADP⁺.In contrast GalE does not release NAD⁺ during the catalytic cycle andthe nicotinamide dinucleotide is less solvent exposed.

For the next 150 residues of GFS there are only minor changes betweenthe two protein in the positions of loops and flanking helices until His170 where there is a 6 residue insertion that extends GalE further intothe solvent. Following this there is a helix in the substrate bindingdomain (helix F in GFS) that superimposes well with GalE and then twostrands (corresponding to strands 7 and 11 in GFS), shown at the top ofFIG. 3, that have both moved. These strands give the substrate bindingregion of GFS a more open, solvent exposed configuration and lack the“flap” in GalE that interacts with the substrate. From modeling ofGDP-4-keto, 6-deoxy mannose binding to GFS (see below) some movement ofresidues within these loops may occur, as has been seen for other SDRenzymes [19]. The only remaining large difference between the twostructures is an insertion of a helix from Ala228-Asn235 in GFS. Thisinsertion is far from substrate or cofactor binding and therefore hasunknown function.

In solution GFS exists as a dimer both from dynamic light scattering andsize exclusion chromatography (data not shown). In the crystal latticeGFS exists as a crystallographic dimer and has an extensivemonomer-monomer interface, burying 1530 Å² of water accessible surfaceper monomer, as calculated with the CCP4 programs AREAMOL and RESAREA[20]. The core of the dimer interface is formed by a four helix bundleconsisting of the flanking helices D and E interacting with themselvesthrough a two fold rotation. This interface also includes some contactsbetween the loop Leu125-Leu129. The predominant interactions are betweenhydrophobic side chains on the long flanking helices along with severalhydrogen bonds at the periphery of the interface. This extensiveinterface presumably explains why the monomer is not observed insolution. Multimerization through a four helix bundle motif is a commonfeature in the SDR family with GalE [21, 22], 17 beta-hydroxysteroiddehydrogenase [23], and Dihydropteridine reductase [24] being typicalexamples of dimers formed this way.

NADP(H) Binding

We obtained binary complexes with both NADP⁺ or NADPH bound to GFS.NADP⁺ lies against one face of the central beta-sheet with theN-terminal end of the first helix in GFS directed towards one of theadenine phosphoryl oxygens (FIGS. 2, 3, and 5 a). NADP+binds in anextended conformation, such that it contacts almost every beta-strandand positions the nicotinamide ring in close proximity to the catalyticdomain. The adenine and nicotinamide ribose conformations are C2′ endoand C3′ endo, respectively, with the nicotinamide ring in the anticonformation with respect to the ribose ring. The interactions made withthe protein are a combination of direct and water mediated hydrogenbonds together with some hydrophobic interactions. The adenine ringpacks between the side chain of Arg36 and the side chains of Leu41,Ala63 and Ile86. Arg36, which is disordered in the NADP⁺ free structure,also makes hydrogen bonds with the ribose phosphoryl oxygens (Nε-OP3 andNH2-OP3 2.5 Å and 2.4 Å respectively). The only hydrogen bond to theadenine moiety is from the N6 to the OD1 of Asn40. One other phosphoryloxygen also makes a water mediated hydrogen bond to the N of Arg36. Theremaining water mediated hydrogen bond is between the adenine ribose O3to the N of Arg12. The interactions with the phosphate groups aresimilar to the characteristic NAD(P) binding domains of thedehydrogenases (Lesk, 1995). The turn between the end of the N-terminalstrand and the N-terminal helix contains the characteristic GXXGXXGmotif also observed in the structure of GalE. The phosphates lie withinthe helix dipole at the N-terminal end of the first helix and makehydrogen bonds with the N atoms of Met14 (2.8 Å) and Val15 (2.8 Å). Thenicotinamide ribose hydroxyls make potential hydrogen bonds with the OHof Tyr136 (2.8 Å), the Nε of Lys140 (3.0 Å) and the carbonyl oxygen ofGly106 (2.3 Å). The nicotinamide ring packs against Leu166 and makespotential hydrogen bonds with the OGs of Ser107 (2.7 Å) and Ser108 (2.7Å) and the N of Ser108 (3.3 Å). A comparison between the NADP⁺ free andbound complexes shows that there are surprisingly few structural changesin GFS upon dinucleotide binding.

The alignment of E. coli and human GFS reveals that all residuesinvolved in NADP⁺ binding mentioned above are identical to or replacedwith conservative substitutions in the human enzyme. The exception isArg36 of the E. coli enzyme which is replaced by Phe40 in the humansequence. Arg36 coordinates the 2′ phosphate group NADP⁺, therebyallowing the enzyme to discriminate between NADP⁺ and NAD⁺. Theinability of phenylalanine to make the necessary contacts allowing theenzyme to distinguish between NADP⁺ and NAD⁺, suggests that the localstructures of the two enzymes differ in this area. At this time it wecannot say which residues in the human enzyme interact with the 2′phosphate group of NADP⁺.

The structure of bound NADPH is superimposable on that of NADP⁺ exceptfor the nicotinamide ring, which rotates into the syn conformationrelative to the ribose ring (FIG. 5 b) and hydrogen bonds withphosphoryl oxygen. Inspection of the electron density (FIG. 8 c)revealed the expected slight puckering of the nicotinamide ring. As aconsequence of this nicotinamide ring rotation, the hydrogen bonds withresidues Ser107 and Ser108 are broken and two water molecules move intothe site. One water molecule replaces the interactions made with the N7and O7 and the other hydrogen bonds with Tyr136 OH and Ser107 OG.

NADPH binding in the syn confirmation allows transfer of the pro-Shydride (B-side) during catalysis. This accords with the knownstereochemistry of the hydride transfer, (R. Kumar and G.-Y. Xu,personal communication). Transfer of the pro-S hydride is a generalfeature of SDR enzymes and NAD(P) has been shown to bind in the synconformation in the structures of all the SDR enzymes solved to date[19, 22, 24-31]. In contrast, the product of the GDP-fucose synthetasereaction, NADP+, binds in the anti confirmation. It is conceivable thatthe different binding mode for substrate and product may help to accountfor the difference in affinity between the two and help promote productrelease. However the gain of H-bonds to the O7 and N7 of thenicotinamide ring in the binding of the product, NADP⁺, relative to thesubstrate, NAPH, does not support this hypothesis. It seems more likelythat the binding of NADP⁺ in the anti conformation is an artifact ofbinding in the absence of the GDP-sugar substrate. The modelingdescribed below suggests that the Ser107-Ser108 could move to interactwith the mannose ring when substrate binds and that the anticonformation seen for NADP⁺ is a consequence of an empty substratebinding site. UDP-glucose-4-epimerase also gave complexes with thenicotinamide ring bound in either syn or anti confirmation dependingupon the oxidation state of the cofactor, although in contrast to GFSthe reduced cofactor was bound in the anti conformation. [18, 22].However, in the structure of the ternary complex of GalE with UDP-sugarsubstrates, NADH bound in the syn conformation, the proper orientationto carry out hydride transfer [32. 33].

Substrate Binding and the Catalytic Site.

Attempts to soak the GDP-4-keto, 6-deoxy mannose substrate or GDP intothe crystals failed so a crude model of GDP-sugar binding was generated(FIG. 6), based on the ternary complexes of GalE [32, 33, 34].GDP-4-keto, 6-deoxy mannose was modeled in QUANTA and minimized withCHARM. The resulting structure was aligned with UDP-glucose in GalE (PDBaccession 1KVU), then moved to optimize the hydrogen bond between thealpha phosphoryl oxygen and the N of Val 180. Some adjustments oftorsion angles within GDP-4-keto, 6-deoxy mannose were made to relievesome bad contacts and maximize van der Waals interacts. This model canbe used to predict which residues may be important for substrate bindingand catalysis. In the model, the Guanine ring of the GDP-sugar substratelies in a hydrophobic pocket made by the side chains of Leu184, Val201,and Val180 and lies next to Trp202. In GalE this tryptophan is replacedby a phenylalanine which partially covers the bound substrate. WhenGDP-4-keto, 6-deoxy mannose binds to GFS this tryptophan may also moveto partially bury the substrate. The N of Val 180 hydrogen bonds to aguanosine phosphoryl oxygen which lies at the N-terminal end of helixVal180-Ala193. The model predicts that Lys283 and Arg209 may be involvedin phosphate binding and that Ser107, Ser108, Cys109 and Asn165 makeinteractions with the 4-keto sugar. The remaining side chain His 179 isin proximity to act as the general acid or base during catalysis. Themodel also places the ketone oxygen within 4 Å of the nicotinaimde ring,in close proximity and in the proper orientation for hydride transfer.The conserved catalytic triad, residues Ser107, Tyr136, and Lys140,occupy similar positions as in the GalE structure and are positioned toplay a role in catalysis (see below).

Mechanisms of the Reactions

A common theme in the reactions catalyzed the GalE and other SDR enzymesis the role played by the conserved Ser-Tyr-Lys. In the proposedmechanism, the pKa of the catalytic tyrosine is lowered via interactionswith the positively charged lysine, the ribose hydroxyls of thenicotinamide, and potentially the catalytic serine [19, 22, 23, 26 27,34]. This allows the tyrosine to play the role of a general acid or basedepending upon the reaction being catalyzed. The catalytic serine mayalso interact with the substrate stabilizing its conformation. Thismechanism is supported by the structure of ternary complexes of GalEwith NADH and UDP-sugars [18, 22, 32, 33] and mutagensis experimentswith GalE [34, 35], as well as the structure of ternary complexes ofother SDR enzymes [19, 26, 27] and mutagenesis of other SDR familymembers [36-40]. In GFS, Ser107, Tyr136, and Lys140 are properlypositioned to play an analogous role in the epimerization and reductionsreactions the enzyme catalyzes. In the GFS structure we find thedistance between NC of Lys140 and the hydroxyl of Tyr136 (4.1 Å) is toofar to stabilize the negative charge on the tyrosine hydroxyl byhydrogen bond interaction. Instead, as has been proposed for other SDRenzymes, Lys 140 helps to stabilize the nicotinamide substrate in anactive conformation through interactions with the ribose hydroxyls andmay help lower the pKa of Tyr136 through electrostatic effects [19, 26,27, 34].

In contrast to GalE and other SDR enzymes, GDP-fucose synthetasecatalyzes two distinct sets of reactions, the epimerizations of C3 andC5 of the 4-keto, 6 deoxy-mannose ring and the NADPH dependent reductionat C4. The epimerizations at C3 and C5 differ from the epimerizationreaction catalyzed by GalE, in that they do not involve the transientreduction and oxidation of an NAD⁺ or NADP⁺ cofactor. The epimerizationscatalyzed by GFS most likely proceed through the enediol/enolateintermediate as first proposed by Ginsberg [41]. The same mechanism hasbeen proposed for the epimerization reactions in the synthesis ofrelated deoxy and dideoxy sugar-nucleotides (reviewed in [14, 42]).

In the epimerization catalyzed by GFS we propose that Tyr136, by virtueof its lowered pKa, plays the role of a general acid during catalysis.It transiently protonates the C4 oxygen, thereby stabilizing theenediol/enolate intermediate. The side chain of His 179, as noted above,could fulfil the role of a general base in one of the reactions,abstracting a proton from C3 or C5 of the intermediate, followed byreprotonation from the opposite face of the sugar ring. Deprotonation ofthe C4 oxygen by Tyr136 acting as a general base completes theepimerization reaction. Lacking the structure of the ternary complex wecannot identify the other residues that function as active site acids orbases. This mechanism is consistent with the observed loss of the C3proton during GFS catalyzed epimerization [10] and with the ability ofGFS to catalyze the epimerization reactions in the absence of NADPH andsubsequent reduction at C4 (F. Sullivan unpublished data).

The other reaction catalyzed by GFS, the NADPH dependent reduction at C4of the 4-keto, 6-deoxy-mannose ring, is more typical of reactionscatalyzed by SDR enzymes. Here we propose that Tyr136, acts as a generalacid and protonates the C4 oxygen in concert with hydride transfer to C4from NADPH. Ser107 may play role in this reaction acting a protonshuttle or in stabilizing the conformation of the substrate in theactive site, both of which have been suggested for other SDR enzymes[19, 26, 27, 34]. The common roles suggested for Tyr136 in theepimerization and reduction reactions are diagramed in FIG. 7. Itprovides the mechanistic continuity between the distinct epimerizationand reduction reactions and suggests how they may be facilitated at thesingle active site in GFS. The details of the both the epimerization andreduction reactions should be clarified by identification of a newcrystal form of GFS which binds both the NADP(H) and GDP-sugarsubstrates and site directed mutagenesis of the implicated residues.

The residues in the substrate binding site are almost completelyconserved between human and the E. coli sequences (FIG. 4). Theexception is Ser108 which is replaced with a conservative threoninemutation. Given the sequence similarity in the residues in the activesites of the human and E. coli enzymes, the E. coli structure may be areasonable starting point to identify possible inhibitors of humanGDP-fucose synthetase.

Both Enzymes Involved in GDP-Fucose Biosynthesis Evolved from a CommonPrecursor.

Comparison of amino acid sequences reveals that the first enzyme inGDP-fucose biosynthesis, GDP-mannose 4,6 dehydratase, is as closelyrelated to GDP-fucose synthetase (24% identity) as it is to UDP-glucose4-epimerase (24% identity). GDP-mannose 4,6 dehydratase also containsthe conserved Ser-Tyr-Lys catalytic triad. This suggests that all threeenzymes have closely related structures and that both the enzymesinvolved in GDP-fucose biosynthesis evolved from a single ancestralgene. Additionally, it is interesting to note that the NADP⁺ in GMD istransiently reduced and then reoxidized in the course of the reactioncycle, a role analogous to the one played by of NAD⁺ in GalE. Bothenzymes are known to bind their cofactors tightly during the catalyticcycle in order to prevent release of the transiently reducednicotinamide [43]. Comparison of their sequences reveals that the loopthat is thought to be responsible for the tight binding of cofactor inGalE, residues Leu33-Phe54 (FIG. 4), while absent in GFS, is present inGMD (data not shown). We predict that these residues also form a flap inGMD to provide additional interaction to keep the NADP⁺ tightly boundduring the catalytic cycle.

Biological Implications

Fucose is found in the glycoconjugates of bacteria, plants and animalswhere it plays roles in maintaining structural integrity as well as inmolecular recognition. Defects in GDP-fucose biosynthesis have beenshown to affect nodulation in bacteria, stem development in plants andimmune regulation in humans. GDP-fucose is synthesized from GDP-mannoseby two enzymes, a NADP⁺ dependent dehydratase and a dual function NADPHdependent epimerase-reductase, GDP-fucose synthetase. In this latteraspect biosynthesis of fucose differs from that of other deoxy sugarswhich utilize separate epimerase and reductase enzymes.

Here we report the structure of E. coli GDP-fucose synthetase and binarycomplexes with NADP⁺ and NADPH. This has allowed us to identifyinteractions involved in binding the NADPH substrate and to suggest thelocation of the binding site for the GDP-sugar substrate. Based uponthese structures it appears that the enzyme contains a single activesite that catalyzes both the epimerization and NADPH dependent reductionreactions. The residues in the active sites of the human and E. coliGDP-fucose synthetase are highly conserved. Thus the present structureof E. coli enzyme could serve as a starting point for the design ofinhibitors of the human enzyme, which ultimately could lead to thedesign of immunosuppressants that act by blocking selectin mediated celladhesion.

Material and Methods

Protein Purification and Crystallization

GFS protein was purified from an E. coli strain over-expressing the E.coli fcl gene, essentially as described by Sullivan et al. [9]. Anadditional step was added to the purification. The protein pool from theHeparin toyapearl step was made 1 M in (NH₄)₂SO₄ and loaded onto aPolypropyl A column (PolyLC). The column was eluted with a gradient from1 to 0 M (NH₄)₂SO₄. The resulting protein was found to be monodisperseby light scattering analysis (DynaPro-801) and have a molecular weightconsistent with a dimer. Similar results were obtained by gel filtrationchromatography on a G3000 column (TosoHass). Crystals measuring0.5×0.5×0.5 mm were obtained within one week using the vapor diffusionhanging drop method. Hanging drops were set up by adding 10 ul of a 6mg/mL protein solution in 10 mM, pH 7.4 Tris buffer, 50 mM sodiumchloride to 10 ul of the well solution consisting of 4.0M sodiumformate.

Data Collection and Processing

Diffraction data were collected using a Raxis II detector mounted on anRU200 X-ray generator running at 50 KV, 100 mA, with the MSC/Yalefocusing mirrors. All data collections were performed at 18° C. withexposure times between 8 and 12 minutes per one degree oscillation. Thedata were reduced with DENZO/SCALEPACK [44] giving unit cell parametersof a=104.2 Å and c=74.9 Å and symmetry P3₂21 or P3₁21. The data aresummarized in Table 1. The CCP4 suite of programs [20] were used for allfurther data processing leading up to heavy atom refinement.

MIRAS Phasing

Initial attempts to solve the structure using molecular replacement withthe homologous GalE structure as a search model failed. A similarattempt at molecular replacement by Tonetti et al. using data fromsimilar crystals of GFS also was unsuccessful [45]. The structure wasdetermined using three heavy atom derivatives. Crystals were soaked for48 hr. in three different heavy metal salts, 5 mM gold potassiumcyanide, 2 mM mercury acetate and 5 mM cadmium chloride, all dissolvedin a 4.2M sodium formate crystal stabilization solution. The primarymercury acetate heavy atom position was determined by inspection of thePatterson function Harker sections and refined using MLPHARE [20]. Oneheavy atom site for the gold derivative and two sites for the cadmiumwere located with difference Fouriers. The space group was found to beP3₂21 giving maps with good solvent protein boundaries and density thatcorresponded to many of the secondary structural elements of GalE. Thegold and mercury heavy atom derivatives had single well occupied heavyatom sites close to Cys 249 in the final model, giving maps that wereinterpretable but with many main chain breaks. An additional heavy metalbinding site was seen in the cadmium derivative. Heavy atom refinementin SHARP [46] revealed several minor sites for each derivative and afinal figure of merit of 0.75 and 0.81 for acentric and centricreflections respectively. After density modification in SOLOMON [47]using a solvent content of 60%, the final figure of merit for allreflections was 0.93. These maps were very high quality with no mainbreaks for the entire molecule (FIG. 8 a)

Model Building and Refinement

The model was built into the experimental maps using QUANTA (MolecularSimulations Inc.). Large pieces of GalE were used to assist with themodel building by changing the side chain identities and moving residuesand secondary structural elements. The resulting model had no breaks inthe backbone and was refined using XPLOR positional, torsion angledynamics, and B-factor refinement giving a final model with statisticsshown in Table 2. The final model consists of residues Lys3 to Phe319with the first and last two residues not visible in the electron densitymaps. The side chains of Arg36, Asp37, Arg55 and His 174 are alsodisordered and were modeled as alanines in the final structure. The sidechains of Arg36 and Asp37 became well ordered upon binding NADP+ orNADPH and were therefore included in those complex models.

Obtaining NADP and NADPH Bound Complexes

The complex of GFS with NADP⁺ was obtained by placing the crystals into4.2M sodium formate, 1 mM NADP⁺ for 20 hours. The resulting complex wasfound to be isomorphous with cell parameters a=104.2 Å and c=75.1 Å.After rigid body refinement of the protein model in XPLOR [48] cleardensity was identified for the bound ligand in both 2F_(O)−F_(C) andF_(O)−F_(C) electron density maps. A model of the complex was builtusing QUANTA and side chains were adjusted to fit the new electrondensity. Refinement of the complex was performed using positional andB-factor refinement in XPLOR, giving a final model with statistics inTable 2.

The isomorphous complex with NADPH was produced by soaking existingcrystals. A 3 mM stock of NADPH was made in the 4.2M sodium formatesolution and fully reduced by the addition of 100 mM sodium borohydride.After 10 hours the crystal was placed into the resulting solution,soaked for 20 hours and then diffraction data were collected usingmethods described above. The crystal had cell parameters a=104.3 Å andc=74.9 Å and also gave clear electron density for NADPH in the resultingmaps. This complex was refined using similar methods to the NADP⁺ boundform.

Accession Numbers

The coordinates of the apo enzyme structure, the NADP⁺ complex, andNADPH complex have been deposited in the Protein Data Bank (entry codes1GFS, 1FXS, and 1BSV).

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1. Crystalline GFS.
 2. The crystalline GFS of claim 1 wherein said GFSis E. coli GFS.
 3. The crystalline GFS of claim 1 wherein said GFS isrecombinant GFS.
 4. The crystalline GFS of claim 1 wherein said GFS iscrystallized with a co-factor selected from the group consisting ofNADPH and NADP+.
 5. The crystalline GFS of claim 1 wherein said GFScomprises the mature sequence of naturally-occurring GFS.
 6. Acrystalline composition comprising GFS is association with a secondchemical species.
 7. The composition of claim 6 wherein said secondchemical species is selected from the group consisting of NADPH, NADP+and a potential inhibitor of GFS activity.
 8. A model of the structureof GFS comprising a data set embodying the structure of crystalline GFSof claim
 1. 9. The model of claim 8 wherein said data set was determinedby crystallographic analysis of GFS.
 10. The model of claim 8 whereinsaid data set was determined by NMR analysis of GFS.
 11. The model ofclaim 8 wherein said data set embodies the entire structure of GFS. 12.The model of claim 8 wherein said data set embodies a portion of thestructure of GFS.
 13. The model of claim 12 wherein said portion is theactive site of GFS.
 14. The model of claim 8 wherein said GFS iscomplexed with a second chemical species selected from the groupconsisting of NADPH, NADP+ and a potential inhibitor of GFS activity.15. A computer system comprising computer hardware and the model ofclaim
 8. 16. A method of identifying a species which is an agonist orantagonist of GFS activity or binding comprising: (a) providing themodel of claim 8, (b) studying the interaction of candidate species withsuch model, and (c) selecting a species which is predicted to act assaid agonist or antagonist.
 17. A species identified in accordance withthe method of claim
 16. 18. A process of identifying a substance thatinhibits GFS activity or binding comprising determining the interactionbetween a candidate substance and a model of claim
 8. 19. A method ofidentifying inhibitors of GFS activity by rational drug designcomprising: (a) designing a potential inhibitor that will formnon-covalent bonds with one or more amino acids in the GFS sequencebased upon the crystal structure co-ordinates of crystalline GFS ofclaim 1; (b) synthesizing the inhibitor; and (c) determining whether thepotential inhibitor inhibits the activity of GFS.
 20. The method ofclaim 19 wherein said inhibitor is designed to interact with one or moreamino acids in the GFS sequence selected from the group consisting ofArg12, Met14, Val15, Arg36, Asn40, Leu41, Ala63, Ile86, Gly106, Ser107,Ser108, Cys109, Tyr136, Lys140, Asn165, Leu166, His179, Val180, Leu184,Val201, Trp202, Arg209, and Lys283.
 21. An agonist or antagonistidentified by the method of claim
 19. 22. A substance identified by themethod of claim
 18. 23. A method of identifying a species which is anagonist or antagonist of human FX protein or binding comprising: (a)providing the model of claim 8, (b) studying the interaction ofcandidate species with such model, and (c) selecting a species which ispredicted to act as said agonist or antagonist.
 24. A species identifiedin accordance with the method of claim
 23. 25. A process of identifyinga substance that inhibits human FX protein activity or bindingcomprising determining the interaction between a candidate substance anda model of claim
 8. 26. A method of identifying inhibitors of human FXprotein activity by rational drug design comprising: (a) designing apotential inhibitor that will form non-covalent bonds with one or moreamino acids in the GFS sequence based upon the crystal structureco-ordinates of crystalline GFS of claim 1; (b) synthesizing theinhibitor; and (c) determining whether the potential inhibitor inhibitsthe activity of human FX protein.
 27. The method of claim 26 whereinsaid inhibitor is designed to interact with one or L-=more amino acidsin the GFS sequence selected from the group consisting of Arg12, Met14,Val15, Arg36, Asn40, Leu41, Ala63, Ile86, Gly106, Ser107, Ser108,Cys109, Tyr136, Lys140, Asn165, Leu166, His179, Val180, Leu184, Val201,Trp202, Arg209, and Lys283.
 28. An agonist or antagonist identified bythe method of claim
 26. 29. A substance identified by the method ofclaim 25.